cool-seq-tool 0.7.1__tar.gz → 0.9.0__tar.gz

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.7.1
+Version: 0.9.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,7 +53,7 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.1.3
+Requires-Dist: wags-tails~=0.2.2
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.7.1; extra == "dev"
@@ -61,11 +61,11 @@ Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
-Requires-Dist: mock; extra == "test"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
@@ -76,10 +76,10 @@ Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 
 <h1 align="center">
-CoolSeqTool
+Cool-Seq-Tool
 </h1>
 
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
 
 ---
 
@@ -90,18 +90,18 @@ CoolSeqTool
 ## Overview
 
 <!-- description -->
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
 <!-- /description -->
 
 ---
 
 ## Install
 
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 
 ```shell
 python3 -m pip install cool-seq-tool
@@ -113,7 +113,7 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/stable/in
 
 ## Usage
 
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
 
 ```pycon
 >>> from cool_seq_tool import CoolSeqTool

cool_seq_tool-0.9.0/README.md

@@ -0,0 +1,59 @@
+<h1 align="center">
+Cool-Seq-Tool
+</h1>
+
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
+**[Documentation](https://coolseqtool.readthedocs.io/stable/)** · [Installation](https://coolseqtool.readthedocs.io/stable/install.html) · [Usage](https://coolseqtool.readthedocs.io/stable/usage.html) · [API reference](https://coolseqtool.readthedocs.io/stable/reference/index.html)
+
+---
+
+## Overview
+
+<!-- description -->
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
+
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
+<!-- /description -->
+
+---
+
+## Install
+
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+
+```shell
+python3 -m pip install cool-seq-tool
+```
+
+See the [installation instructions](https://coolseqtool.readthedocs.io/stable/install.html) in the documentation for a description of dependency setup requirements.
+
+---
+
+## Usage
+
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
+
+```pycon
+>>> from cool_seq_tool import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
+>>> cst = CoolSeqTool()
+>>> result = await cst.mane_transcript.get_mane_transcript(
+...     "NP_004324.2",
+...     599,
+...     AnnotationLayer.PROTEIN,
+...     coordinate_type=CoordinateType.INTER_RESIDUE,
+... )
+>>> result.gene, result.refseq, result.status
+('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
+```
+
+---
+
+## Feedback and contributing
+
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/stable/contributing.html) contains guidance for submitting feedback and contributing new code.

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/docs/source/contributing.rst

@@ -17,7 +17,7 @@ Create a virtual environment and install :ref:`all dependency groups<dependency-
 
     python3 -m venv venv
     source venv/bin/activate
-    python3 -m pip install -e ".[dev,test,docs]"
+    python3 -m pip install -e ".[dev,tests,docs]"
 
 We use `pre-commit <https://pre-commit.com/#usage>`_ to run conformance tests before commits. This provides checks for:
 

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/docs/source/index.rst

@@ -16,15 +16,15 @@ Cool-Seq-Tool |version|
    :alt: tests status
    :target: https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml
 
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
-* A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, `MANE transcript <https://www.ncbi.nlm.nih.gov/refseq/MANE/>`_ descriptions, and the `Universal Transcript Archive <https://github.com/biocommons/uta>`_
+* A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, `MANE transcript <https://www.ncbi.nlm.nih.gov/refseq/MANE/>`_ descriptions, and transcript alignment data from the `Universal Transcript Archive <https://github.com/biocommons/uta>`_
 * Augmented access to the `SeqRepo <https://github.com/biocommons/biocommons.seqrepo>`_ database, including multiple additional methods and tools
-* Mapping tools that combine the above to support translation between various references sequences and annotation layers, and to MANE-designated transcripts
+* Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined :ref:`here <transcript_selection_policy>`, that combine the above to support translation between various references sequences and annotation layers, and transcripts
 
 See the :ref:`Installation <installation>` and :ref:`Usage <usage>` pages for information on getting started. Individual classes and methods are documented within the :ref:`API reference <api_reference>`.
 
-CoolSeqTool was created to support the `Knowledgebase Integration Project <https://cancervariants.org/projects/integration/>`_ of the `Variant Interpretation for Cancer Consortium (VICC) <https://cancervariants.org/>`_. It is developed primarily by the `Wagner Lab <https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab>`_. Full source code is available on `GitHub <https://github.com/genomicmedlab/cool-seq-tool>`_.
+Cool-Seq-Tool was created to support the `Knowledgebase Integration Project <https://cancervariants.org/projects/integration/>`_ of the `Variant Interpretation for Cancer Consortium (VICC) <https://cancervariants.org/>`_. It is developed primarily by the `Wagner Lab <https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab>`_. Full source code is available on `GitHub <https://github.com/genomicmedlab/cool-seq-tool>`_.
 
 .. toctree::
    :hidden:

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/docs/source/install.rst

@@ -24,7 +24,7 @@ Install Cool-Seq-Tool from `PyPI <https://pypi.org/project/cool-seq-tool/>`_:
    Cool-Seq-Tool provides extra dependency groups for development and testing purposes. Most users won't need to install them.
 
    * ``dev`` includes packages for linting and performing other kinds of quality checks
-   * ``test`` includes packages for running tests
+   * ``tests`` includes packages for running tests
    * ``docs`` includes packages for writing and building documentation
 
 Set up UTA

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/docs/source/transcript_selection.rst

@@ -28,8 +28,9 @@ All compatible transcripts are evaluated and ordered against the below criteria.
 #. Transcript is annotated as a `MANE Select` transcript
 #. Transcript is annotated as a `MANE Plus Clinical` transcript
 #. Transcript is the longest-compatible remaining transcript
-#. Transcript is the first-published (lowest-numbered RefSeq/Ensembl accession) remaining transcript
 
-.. note::
+   #. If there is a tie, choose the first-published (lowest-numbered RefSeq/Ensembl accession) transcript
 
-   We always prefer the most recent version of a transcript associated with an assembly.
+   .. note::
+
+      We always prefer the most recent version of a transcript associated with an assembly.

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/docs/source/usage.rst

@@ -30,7 +30,7 @@ Descriptions and examples of functions can be found in the :ref:`API Reference <
 
 .. note::
 
-   Many component classes in CoolSeqTool, including :py:class:`UtaDatabase <cool_seq_tool.sources.uta_database.UtaDatabase>`, :py:class:`ExonGenomicCoordsMapper <cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper>`, and :py:class:`ManeTranscript <cool_seq_tool.mappers.mane_transcript>`, define public methods as ``async``. This means that, when used inside another function, they must be called with ``await``:
+   Many component classes in Cool-Seq-Tool, including :py:class:`UtaDatabase <cool_seq_tool.sources.uta_database.UtaDatabase>`, :py:class:`ExonGenomicCoordsMapper <cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper>`, and :py:class:`ManeTranscript <cool_seq_tool.mappers.mane_transcript>`, define public methods as ``async``. This means that, when used inside another function, they must be called with ``await``:
 
    .. code-block:: python
 

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/pyproject.toml

@@ -33,14 +33,14 @@ dependencies = [
     "biocommons.seqrepo",
     "pydantic == 2.*",
     "ga4gh.vrs ~= 2.0.0a10",
-    "wags-tails ~= 0.1.3",
+    "wags-tails ~= 0.2.2",
     "bioutils",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = ["pre-commit>=3.7.1", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
-test = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
+tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/src/cool_seq_tool/mappers/exon_genomic_coords.py

@@ -87,7 +87,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
     """Model for representing a boundary for a transcript segment."""
 
     seg: TxSegment | None = Field(None, description="Transcript segment.")
-    gene: StrictStr | None = Field(None, description="HGNC gene symbol.")
+    gene: StrictStr | None = Field(
+        None, description="Valid, case-sensitive HGNC gene symbol."
+    )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
     errors: list[StrictStr] = Field([], description="Error messages.")
@@ -139,7 +141,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
 class GenomicTxSegService(BaseModelForbidExtra):
     """Service model for genomic and transcript data."""
 
-    gene: StrictStr | None = Field(None, description="HGNC gene symbol.")
+    gene: StrictStr | None = Field(
+        None, description="Valid, case-sensitive HGNC gene symbol."
+    )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
     seg_start: TxSegment | None = Field(None, description="Start transcript segment.")
@@ -292,7 +296,7 @@ class ExonGenomicCoordsMapper:
         ('NC_000001.11', 154192135, 154170399)
 
         :param transcript: RefSeq transcript accession
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param exon_start: Starting transcript exon number (1-based). If not provided,
             must provide ``exon_end``
         :param exon_start_offset: Starting exon offset
@@ -335,9 +339,6 @@ class ExonGenomicCoordsMapper:
         if errors:
             return _return_service_errors(errors)
 
-        if gene:
-            gene = gene.upper()
-
         # Get aligned genomic data (hgnc gene, alt_ac, alt_start_i, alt_end_i, strand)
         # for exon(s)
         (
@@ -455,7 +456,7 @@ class ExonGenomicCoordsMapper:
             following the breakpoint for the 3' end. For the negative strand, adjacent
             is defined as the exon following the breakpoint for the 5' end and the exon
             preceding the breakpoint for the 3' end.
-        :param gene: gene name. Ideally, HGNC symbol. Must be given if no ``transcript``
+        :param gene: A valid, case-sensitive HGNC symbol. Must be given if no ``transcript``
             value is provided.
         :param coordinate_type: Coordinate type for ``seg_start_genomic`` and
             ``seg_end_genomic``
@@ -473,9 +474,6 @@ class ExonGenomicCoordsMapper:
         if errors:
             return _return_service_errors(errors)
 
-        if gene is not None:
-            gene = gene.upper()
-
         params = {}
 
         if seg_start_genomic:
@@ -630,7 +628,7 @@ class ExonGenomicCoordsMapper:
             must provide ``tx_exon_end``
         :param tx_exon_end: Transcript's exon end coordinates. If not provided, must
             provide ``tx_exon_start``
-        :param gene: HGNC gene symbol
+        :param gene: A valid, case-sensitive HGNC gene symbol
         :return: Tuple containing aligned genomic data for start and end exon and
             warnings if found
         """
@@ -755,7 +753,7 @@ class ExonGenomicCoordsMapper:
         :param transcript: The transcript to use. If this is not given, we will try the
             following transcripts: MANE Select, MANE Clinical Plus, Longest Remaining
             Compatible Transcript
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param get_nearest_transcript_junction: If ``True``, this will return the
             adjacent exon if the position specified by``seg_start_genomic`` or
             ``seg_end_genomic`` does not occur on an exon. For the positive strand, adjacent
@@ -1062,7 +1060,7 @@ class ExonGenomicCoordsMapper:
         :param genomic_ac: Genomic RefSeq accession
         :param genomic_pos: Genomic position where the transcript segment occurs
         :param is_seg_start: Whether or not ``genomic_pos`` represents the start position.
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param tx_ac: Transcript RefSeq accession. If not provided, will use MANE
             transcript
         :return: Transcript segment data and associated genomic metadata
@@ -1171,14 +1169,32 @@ class ExonGenomicCoordsMapper:
         :param end: Genomic coordinate of breakpoint
         :return: Exon number corresponding to adjacent exon. Will be 0-based
         """
-        for i in range(len(tx_exons_genomic_coords) - 1):
+        # If a transcript has only one exon, return 0
+        if len(tx_exons_genomic_coords) == 1:
+            return 0
+
+        # Check if a breakpoint occurs before/after the transcript boundaries
+        bp = start if start else end
+        exon_list_len = len(tx_exons_genomic_coords) - 1
+
+        if strand == Strand.POSITIVE:
+            if bp < tx_exons_genomic_coords[0].alt_start_i:
+                return 0
+            if bp > tx_exons_genomic_coords[exon_list_len].alt_end_i:
+                return exon_list_len
+        if strand == Strand.NEGATIVE:
+            if bp > tx_exons_genomic_coords[0].alt_end_i:
+                return 0
+            if bp < tx_exons_genomic_coords[exon_list_len].alt_start_i:
+                return exon_list_len
+
+        for i in range(exon_list_len):
             exon = tx_exons_genomic_coords[i]
             if start == exon.alt_start_i:
                 break
             if end == exon.alt_end_i:
                 break
             next_exon = tx_exons_genomic_coords[i + 1]
-            bp = start if start else end
             if strand == Strand.POSITIVE:
                 lte_exon = exon
                 gte_exon = next_exon
@@ -1187,6 +1203,7 @@ class ExonGenomicCoordsMapper:
                 gte_exon = exon
             if bp >= lte_exon.alt_end_i and bp <= gte_exon.alt_start_i:
                 break
+
         # Return current exon if end position is provided, next exon if start position
         # is provided.
         return exon.ord if end else exon.ord + 1

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/src/cool_seq_tool/sources/mane_transcript_mappings.py

@@ -61,7 +61,9 @@ class ManeTranscriptMappings:
             location information). The list is sorted so that a MANE Select entry comes
             first, followed by a MANE Plus Clinical entry, if available.
         """
-        data = self.df.filter(pl.col("symbol") == gene_symbol.upper())
+        data = self.df.filter(
+            pl.col("symbol").str.to_uppercase() == gene_symbol.upper()
+        )
 
         if len(data) == 0:
             _logger.warning(

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.7.1
+Version: 0.9.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -53,7 +53,7 @@ Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: ga4gh.vrs~=2.0.0a10
-Requires-Dist: wags-tails~=0.1.3
+Requires-Dist: wags-tails~=0.2.2
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=3.7.1; extra == "dev"
@@ -61,11 +61,11 @@ Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
 Requires-Dist: ruff==0.5.0; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "test"
-Requires-Dist: mock; extra == "test"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"
 Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
@@ -76,10 +76,10 @@ Requires-Dist: furo==2023.3.27; extra == "docs"
 Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 
 <h1 align="center">
-CoolSeqTool
+Cool-Seq-Tool
 </h1>
 
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14007783.svg)](https://doi.org/10.5281/zenodo.14007783) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
 
 ---
 
@@ -90,18 +90,18 @@ CoolSeqTool
 ## Overview
 
 <!-- description -->
-The **CoolSeqTool** provides:
+The Common Operations On Lots-Of Sequences Tool, **Cool-Seq-Tool**, provides:
 
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
+- A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and transcript alignment data from the [Universal Transcript Archive](https://github.com/biocommons/uta)
+- Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
+- Mapping tools, including a transcript selection algorithm for selecting a representative transcript defined [here](https://coolseqtool.readthedocs.io/stable/transcript_selection.html), that combine the above to support translation between references sequences, annotation layers, and transcripts
 <!-- /description -->
 
 ---
 
 ## Install
 
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
+Cool-Seq-Tool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 
 ```shell
 python3 -m pip install cool-seq-tool
@@ -113,7 +113,7 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/stable/in
 
 ## Usage
 
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
+All Cool-Seq-Tool resources can be initialized by way of a top-level class instance:
 
 ```pycon
 >>> from cool_seq_tool import CoolSeqTool

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/SOURCES.txt

@@ -9,7 +9,6 @@ pyproject.toml
 .github/ISSUE_TEMPLATE/bug-report.yaml
 .github/ISSUE_TEMPLATE/feature-request.yaml
 .github/workflows/checks.yaml
-.github/workflows/close_issue.yml
 .github/workflows/pr-priority-label.yaml
 .github/workflows/release.yml
 .github/workflows/stale.yaml

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/src/cool_seq_tool.egg-info/requires.txt

@@ -7,7 +7,7 @@ hgvs
 biocommons.seqrepo
 pydantic==2.*
 ga4gh.vrs~=2.0.0a10
-wags-tails~=0.1.3
+wags-tails~=0.2.2
 bioutils
 
 [dev]
@@ -26,7 +26,7 @@ sphinxext-opengraph==0.8.2
 furo==2023.3.27
 sphinx-github-changelog==1.2.1
 
-[test]
+[tests]
 pytest
 pytest-cov
 pytest-asyncio==0.18.3

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/tests/conftest.py

@@ -277,6 +277,21 @@ def nm_001105539_exons_genomic_coords():
     ]
 
 
+@pytest.fixture(scope="session")
+def mm_001005183_1_exons():
+    """Create test fixture for NM_001005183.1 exons and genomic coordinates"""
+    return [
+        _ExonCoord(
+            ord=0,
+            tx_start_i=0,
+            tx_end_i=939,
+            alt_start_i=55426253,
+            alt_end_i=55427192,
+            alt_strand=Strand.POSITIVE,
+        )
+    ]
+
+
 @pytest.fixture(scope="session")
 def tpm3_1_8_start_genomic():
     """Create test fixture for genomic data for exon 1, 8"""

{cool_seq_tool-0.7.1 → cool_seq_tool-0.9.0}/tests/mappers/test_exon_genomic_coords.py

@@ -806,7 +806,10 @@ async def test_get_start_end_exon_coords(test_egc_mapper):
 
 @pytest.mark.asyncio()
 async def test_get_adjacent_exon(
-    test_egc_mapper, nm_152263_exons_genomic_coords, nm_001105539_exons_genomic_coords
+    test_egc_mapper,
+    nm_152263_exons_genomic_coords,
+    nm_001105539_exons_genomic_coords,
+    mm_001005183_1_exons,
 ):
     """Test that get_adjacent_exon works properly"""
     resp = test_egc_mapper._get_adjacent_exon(
@@ -840,6 +843,41 @@ async def test_get_adjacent_exon(
     )
     assert resp == 4
 
+    # Check cases where breakpoint occurs in before/after transcript boundaries
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80486220,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_001105539_exons_genomic_coords,
+        start=80526285,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 5
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154192110,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 0
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=nm_152263_exons_genomic_coords,
+        end=154161809,
+        strand=Strand.NEGATIVE,
+    )
+    assert resp == 9
+
+    # Check cases where transcript only has one exon and breakpoint does not occur
+    # exon
+    resp = test_egc_mapper._get_adjacent_exon(
+        tx_exons_genomic_coords=mm_001005183_1_exons,
+        start=55411058,
+        strand=Strand.POSITIVE,
+    )
+    assert resp == 0
+
 
 def test_is_exonic_breakpoint(test_egc_mapper, nm_001105539_exons_genomic_coords):
     """Test is breakpoint occurs on exon"""
@@ -1162,7 +1200,7 @@ async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
         "seg_start_genomic": 9597639,
         "seg_end_genomic": 9609996,
         "transcript": "NM_003390.3",
-        "gene": "wee1",
+        "gene": "WEE1",
     }
     g_to_t_resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     genomic_tx_seg_service_checks(g_to_t_resp, wee1_exon2_exon11)
@@ -1177,7 +1215,7 @@ async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
         "genomic_ac": "NC_000011.9",
         "seg_start_genomic": 9597639,  # GRCh38 coords: 9576092
         "seg_end_genomic": 9609996,  # GRCh38 coords: 9588449
-        "gene": "wee1",
+        "gene": "WEE1",
     }
     g_to_t_resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     genomic_tx_seg_service_checks(g_to_t_resp, mane_wee1_exon2_exon11)
@@ -1216,12 +1254,6 @@ async def test_transcript_to_genomic(
     expected.seg_end.genomic_location.start = 154170399
     genomic_tx_seg_service_checks(resp, expected)
 
-    resp = await test_egc_mapper.tx_segment_to_genomic(
-        exon_start=None, exon_end=8, gene="tpm3", transcript="NM_152263.3"
-    )
-    expected.seg_end.genomic_location.start = 154170399
-    genomic_tx_seg_service_checks(resp, expected)
-
     expected = tpm3_exon1_exon8.model_copy(deep=True)
     resp = await test_egc_mapper.tx_segment_to_genomic(
         exon_start=1, exon_end=8, exon_end_offset=-5, transcript="NM_152263.3"
@@ -1371,7 +1403,7 @@ async def test_invalid(test_egc_mapper):
         gene="dummy gene",
     )
     genomic_tx_seg_service_checks(resp, is_valid=False)
-    assert resp.errors == ["Expected gene, DUMMY GENE, but found TPM3"]
+    assert resp.errors == ["Expected gene, dummy gene, but found TPM3"]
 
     # Invalid accession
     resp = await test_egc_mapper.genomic_to_tx_segment(

cool_seq_tool-0.7.1/.github/workflows/close_issue.yml

@@ -1,18 +0,0 @@
-name: Close issues related to a merged pull request based on staging branch.
-
-on:
-  pull_request:
-    types: [closed]
-    branches:
-      - staging
-
-jobs:
-  closeIssueOnPrMergeTrigger:
-
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Closes issues related to a merged pull request.
-        uses: ldez/gha-mjolnir@v1.0.3
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

cool_seq_tool-0.7.1/README.md

@@ -1,59 +0,0 @@
-<h1 align="center">
-CoolSeqTool
-</h1>
-
-[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
-
----
-
-**[Documentation](https://coolseqtool.readthedocs.io/stable/)** · [Installation](https://coolseqtool.readthedocs.io/stable/install.html) · [Usage](https://coolseqtool.readthedocs.io/stable/usage.html) · [API reference](https://coolseqtool.readthedocs.io/stable/reference/index.html)
-
----
-
-## Overview
-
-<!-- description -->
-The **CoolSeqTool** provides:
-
- - A Pythonic API on top of sequence data of interest to tertiary analysis tools, including mappings between gene names and transcripts, [MANE transcript](https://www.ncbi.nlm.nih.gov/refseq/MANE/) descriptions, and the [Universal Transcript Archive](https://github.com/biocommons/uta)
- - Augmented access to the [SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, including multiple additional methods and tools
- - Mapping tools that combine the above to support translation between references sequences, annotation layers, and MANE transcripts
-<!-- /description -->
-
----
-
-## Install
-
-CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
-
-```shell
-python3 -m pip install cool-seq-tool
-```
-
-See the [installation instructions](https://coolseqtool.readthedocs.io/stable/install.html) in the documentation for a description of dependency setup requirements.
-
----
-
-## Usage
-
-All CoolSeqTool resources can be initialized by way of a top-level class instance:
-
-```pycon
->>> from cool_seq_tool import CoolSeqTool
->>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
->>> cst = CoolSeqTool()
->>> result = await cst.mane_transcript.get_mane_transcript(
-...     "NP_004324.2",
-...     599,
-...     AnnotationLayer.PROTEIN,
-...     coordinate_type=CoordinateType.INTER_RESIDUE,
-... )
->>> result.gene, result.refseq, result.status
-('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
-```
-
----
-
-## Feedback and contributing
-
-We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/stable/contributing.html) contains guidance for submitting feedback and contributing new code.